I In this study, allelic polymorphism in candidate genes of TLR4 and IL2 involved in the immune system in four Iranian indigenous chickens were examined using PCR-RFLP technique. A total of 200 birds including common, West Azerbaijan, Marandi, Mazandarani indigenous chicken breeds were selected. For detection of mutation in TLR4 (257 bp) and IL2 (600 bp) genes the PCR products were digested by Sau96I and HphI restriction enzymes, respectively. Two alleles of C (138 and 119 bp) and G (119, 99 and 39 bp) and three genotypes of CC, CG and GG were identified in TLR4 marker site. Following the enzymatic digestion of the IL2 gene, two alleles of A (465, 64, 40 and 31bp) and B (454, 64, 40, 31 and 11 bp) and three genotypes of AA, AB and BB were identified. The whole populations was in Hardy-Weinberg equilibrium for TLR4 and IL2 marker sites. The calculated Shannon information index and fixation index values for TLR4 and IL2 marker sites was estimated to be (0.56 and 0.69) and (-0.05 and -0.10), respectively. The highest observed heterozygosity value for TLR4 and IL2 loci was estimated to be (0.55 and 0.40), respectively. Regarding to the existence of polymorphism in the studied loci and reduction of heterozygosity in these populations, the occurrence of non-random crosses can be prevented. This leads to an increase in heterozygosity and thus prevents the loss of genetic diversity in the populations would be. In the populations also, by studying the immune responses associated with these two loci, these sites can be used as suitable markers in breeding programs for increase of resistance to diseases in indigenous chickens.